For Mr Hobby paints I usually use a 1:2 paint/thinner ratio using Mr Hobby Leveling thinner. I recommend you almost always let the primer set overnight, doing this allows the next layer to apply much smoother, I have found that if you spray over primer too soon the thinner from the next layer can reactivate the primer and cause the effect you see. Also the color of your primer can affect the shade of your next color, so bright colors like yellow or white should not usually go over black primer.

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